## [1] "data/config.vertebrata_minimal.yaml"

Analysis report - 20 January, 2023 - 13:08 UTC - version: 0.9.7

Setup

Location of genomes files:

results/assemblies

Total number of included genomes: 0
Locally provided genomes: 0
Successfully downloaded genomes: 0
Failed species downloads: 0
Not downloaded:

Information on successfully downloaded genomes:

info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
  if (file.size(downloaded_genomes_statistics_file) != 0) {
      data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
  } else {
    info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
  }
  
  data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
  info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}

No information about downloaded genomes found. Did you run phylociraptor setup ?

Orthology

Orthologous genes were inferred using BUSCO.

Location of BUSCO results:

results/orthology/busco

Used BUSCO set: vertebrata_odb10

Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
320238at7742, 164538at7742, 228730at7742

Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:

species single_copy duplicated fragmented missing
Amblyraja_radiata 2999 71 98 186
Anolis_carolinensis 2861 22 169 302
Callorhinchus_milii 2976 34 131 213
Canis_lupus 3122 47 65 120
Danio_kyathit 3107 45 75 127
Dasypus_novemcinctus 2717 61 212 364
Eptatretus_burgeri 1612 59 490 1193
Gallus_gallus 3180 29 45 100
Homo_sapiens 2984 130 77 163
Latimeria_chalumnae 2795 30 279 250
Loxodonta_africana 3039 22 103 190
Meleagris_gallopavo 2872 19 205 258
Monodelphis_domestica 3049 142 76 87
Mus_musculus 3124 55 51 124
Neoceratodus_forsteri 2101 75 723 455
Notamacropus_eugenii 1169 29 514 1642
Oreochromis_niloticus 3275 20 25 34
Ornithorhynchus_anatinus 3075 36 141 102
Petromyzon_marinus 2275 59 193 827
Protopterus_annectens 2029 1130 105 90
Rana_temporaria 3088 74 76 116
Scyliorhinus_canicula 2977 102 106 169
Taeniopygia_guttata 3161 19 50 124
Takifugu_rubripes 3120 77 73 84
Xenopus_tropicalis 3231 34 30 59

Alignments

full

Location of alignment files:

results/alignments/full

Used aligner(s) and settings:
1. clustalo
Parsimony informative sites cutoff: 50

Number of alignments for clustalo: 16

Overview of individual full alignments:
clustalo
length nseqs nparsimony nvariable nfixed
193525at7742_aligned.fas 652 25 179 617 35
359032at7742_aligned.fas 347 25 104 325 22
406935at7742_aligned.fas 291 25 75 275 16
97645at7742_aligned.fas 1237 24 290 1162 75
332227at7742_aligned.fas 554 23 169 508 46
361842at7742_aligned.fas 352 25 74 334 18
409625at7742_aligned.fas 244 25 69 234 10
33940at7742_aligned.fas 1351 25 104 1085 266
378120at7742_aligned.fas 291 25 108 241 50
409719at7742_aligned.fas 367 25 73 345 22
342641at7742_aligned.fas 364 25 128 324 40
403632at7742_aligned.fas 423 25 34 412 11
413149at7742_aligned.fas 232 25 75 226 6
353318at7742_aligned.fas 382 25 89 369 13
404316at7742_aligned.fas 262 25 66 221 41
42971at7742_aligned.fas 1333 23 453 1043 290

trimmed

Location of trimmed alignment files:

results/alignments/trimmed

Parsimony informative sites cutoff: 50


Number of trimmed alignments for clustalo-trimal: 16

Overview of individual trimmed alignments:
clustalo
trimal
alignment length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 454 25 179 419 35
359032at7742_aligned_trimmed.fas 254 25 104 232 22
406935at7742_aligned_trimmed.fas 197 25 75 181 16
97645at7742_aligned_trimmed.fas 747 24 290 672 75
332227at7742_aligned_trimmed.fas 298 23 169 252 46
361842at7742_aligned_trimmed.fas 217 25 74 199 18
409625at7742_aligned_trimmed.fas 137 25 69 127 10
33940at7742_aligned_trimmed.fas 1018 25 104 752 266
378120at7742_aligned_trimmed.fas 253 25 108 203 50
409719at7742_aligned_trimmed.fas 135 25 73 113 22
342641at7742_aligned_trimmed.fas 260 25 128 220 40
403632at7742_aligned_trimmed.fas 166 25 34 155 11
413149at7742_aligned_trimmed.fas 124 25 75 118 6
353318at7742_aligned_trimmed.fas 214 25 89 201 13
404316at7742_aligned_trimmed.fas 212 25 66 171 41
42971at7742_aligned_trimmed.fas 1026 23 453 736 290

filtered

Location of filtered alignment files:

results/alignments/filtered

Parsimony informative sites cutoff: 50


Number of filtered alignments for clustalo-trimal: 15

Overview of individual filtered alignments:
clustalo
trimal
alignment length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 454 25 179 419 35
359032at7742_aligned_trimmed.fas 254 25 104 232 22
409625at7742_aligned_trimmed.fas 137 25 69 127 10
332227at7742_aligned_trimmed.fas 298 23 169 252 46
361842at7742_aligned_trimmed.fas 217 25 74 199 18
409719at7742_aligned_trimmed.fas 135 25 73 113 22
33940at7742_aligned_trimmed.fas 1018 25 104 752 266
378120at7742_aligned_trimmed.fas 253 25 108 203 50
413149at7742_aligned_trimmed.fas 124 25 75 118 6
342641at7742_aligned_trimmed.fas 260 25 128 220 40
404316at7742_aligned_trimmed.fas 212 25 66 171 41
42971at7742_aligned_trimmed.fas 1026 23 453 736 290
353318at7742_aligned_trimmed.fas 214 25 89 201 13
406935at7742_aligned_trimmed.fas 197 25 75 181 16
97645at7742_aligned_trimmed.fas 747 24 290 672 75

Modeltesting

Location of modeltesting files:

results/modeltest
Overview of individual modeltest results:
alignment clustalo-trimal
404316at7742 JTT+R3
406935at7742 VT+G4
97645at7742 JTT+R3
361842at7742 JTTDCMut+G4
413149at7742 JTTDCMut+G4
409719at7742 LG+G4
332227at7742 JTT+G4
42971at7742 JTT+I+G4
409625at7742 JTT+I+G4
193525at7742 JTT+G4
353318at7742 JTT+G4
378120at7742 JTTDCMut+F+R3
342641at7742 LG+I+G4
359032at7742 JTT+I+G4
33940at7742 VT+R2

Genetrees

Location of gene trees:

results/modeltest

Overview of mean bootstrap values per gene-tree:
Total number of gene trees for clustalo-trimal: 15
gene clustalo-trimal
404316at7742 81
406935at7742 75
97645at7742 83
361842at7742 79
413149at7742 77
409719at7742 66
332227at7742 87
42971at7742 87
409625at7742 76
193525at7742 87
353318at7742 83
378120at7742 75
342641at7742 75
359032at7742 78
33940at7742 83

MLtree

Location of phylogenetic results:

results/phylogeny-*/

Overview of concatenated Maximum-likelihood phylogenies:
software aligner trimmer boostraps bootstrap-cutoff ngenes tree
iqtree clustalo trimal 1000 80 7

Speciestree

Location of phylogenetic results:

results/phylogeny-*/

Overview of species-tree phylogenies:
software aligner trimmer bootstrap-cutoff ngenes tree
astral clustalo trimal 80 7

Log

## Fri Jan 20 12:37:08 UTC 2023 - Pipeline part 1 (orthology) done.
## Fri Jan 20 12:37:30 UTC 2023 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Fri Jan 20 12:37:32 UTC 2023 - Number of BUSCO sequence files: 16
## Fri Jan 20 12:37:32 UTC 2023 - Number of deduplicated BUSCO sequence files: 16
## Fri Jan 20 12:37:32 UTC 2023 - Pipeline part filter-orthology done.
## Fri Jan 20 12:39:48 UTC 2023 - Pipeline part 2 (align) done.
## Fri Jan 20 12:40:42 UTC 2023 - Number of alignments (clustalo): 16
## Fri Jan 20 12:40:42 UTC 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Fri Jan 20 12:40:42 UTC 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Fri Jan 20 12:40:46 UTC 2023 - Pipeline part filter_align done.
## Fri Jan 20 12:47:06 UTC 2023 - Pipeline part modeltest (model) done.
## Fri Jan 20 12:48:13 UTC 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Fri Jan 20 12:48:14 UTC 2023 - Speciestree reconstruction done.
## Fri Jan 20 13:03:05 UTC 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Fri Jan 20 13:03:05 UTC 2023 - nexus file for iqtree written.
## Fri Jan 20 13:04:56 UTC 2023 - Pipeline part 3 (tree) done.